Software Citation in Theory and Practice
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The document discusses the critical role of software in research and scholarship, highlighting the need for proper software citation to ensure recognition and attribution for software contributions. It outlines principles for software citation, emphasizing the importance of unique identification, persistence, accessibility, and specificity, and provides examples of good and poor citation practices. The document also details the establishment of software citation working groups and suggests future steps for standardizing software citations across various domains.
![Examples of good citations
• Eigen Project. (2017). Eigen [software] version 3.3.4
Available from https://bitbucket.org/eigen/eigen/
[accessed 2018-04-27]
• Vince Knight, & Ria Baldevia. (2018, January 31).
drvinceknight/Nashpy: v0.0.13 (Version v0.0.13).
Zenodo. http://doi.org/10.5281/zenodo.1163694](https://image.slidesharecdn.com/2018-180725144808/85/Software-Citation-in-Theory-and-Practice-14-320.jpg)
Software Citation in Theory and Practice
- 1. National Center for Supercomputing Applications University of Illinois at Urbana–Champaign Software Citation in Theory and Practice International Congress on Mathematical Software (ICMS 2018) University of Notre Dame, 25 July 2018 Daniel S. Katz* (and Neil Chue Hong) *Assistant Director for Scientific Software & Applications, NCSA Research Associate Professor, CS Research Associate Professor, ECE Research Associate Professor, iSchool dskatz@illinois.edu, d.katz@ieee.org, @danielskatz
- 2. Software in research • Claim: software (including services) essential for the bulk of research • Evidence from surveys • UK academics at Russell Group Universities (2014) • Members of (US) National Postdoctoral Research Association (2017) • My research would not be possible without software: 67% / 63% (UK/US) • My research would be possible but harder: 21% / 31% • It would make no difference: 10% / 6% S. Hettrick, “It's impossible to conduct research without software, say 7 out of 10 UK researchers,” Software Sustainaiblity Institute, 2014. Available at: https://www.software.ac.uk/blog/2016-09-12-its-impossible-conduct- research-without-software-say-7-out-10-uk-researchers S.J. Hettrick, M. Antonioletti, L. Carr, N. Chue Hong, S. Crouch, D. De Roure, et al, “UK Research Software Survey 2014”, Zenodo, 2014. doi: 10.5281/zenodo.14809. U. Nangia and D. S. Katz, “Track 1 Paper: Surveying the U.S. National Postdoctoral Association Regarding Software Use and Training in Research,” WSSSPE5.1, 2017. doi: 10.6084/m9.figshare.5328442.v1
- 3. Software in scholarship • Claim: software (including services) essential for the bulk of research • Evidence from journals: • About half the papers in recent issues of Science were software-intensive projects • In Nature Jan–Mar 2017, software mentioned in 32 of 40 research articles • Average of 6.5 software packages mentioned per article U. Nangia and D. S. Katz, "Understanding Software in Research: Initial Results from Examining Nature and a Call for Collaboration," WSSSPE5.2, 2017. https://doi.org/10.1109/eScience.2017.78
- 4. Software in research cycle Create Hypothesis Acquire Resources (e.g., Funding, Software, Data) Perform Research (Build Software & Data) Publish Results (e.g., Paper, Book, Software, Data) Gain Recognition Knowledge Infrastructure (share and cite) Research
- 5. How to better measure software contributions • Citation system was created for papers/books • We need to either/both 1. Jam software into current citation system 2. Rework citation system • Focus on 1 as possible; 2 is very hard. • Overall challenge: not just to identify software in a paper • To identify software used within research process
- 6. Software citation principles: People & Process • FORCE11 Software Citation group started July 2015 (co-leads Smith & Katz) • WSSSPE3 Credit & Citation working group joined September 2015 (Niemeyer joined as co-lead) • ~60 members (researchers, developers, publishers, repositories, librarians) • Work on GitHub https://github.com/force11/force11-scwg & FORCE11 https://www.force11.org/group/software-citation-working-group • Reviewed existing community practices & developed use cases • Drafted software citation principles document • Started with data citation principles, updated based on software use cases and related work, updated based working group discussions, community feedback and review of draft, workshop at FORCE2016 in April • Discussion via GitHub issues, changes tracked • Submitted, reviewed and modified (many times), now published (with reviews) • Smith AM, Katz DS, Niemeyer KE, FORCE11 Software Citation Working Group.(2016) Software Citation Principles. PeerJ Computer Science 2:e86. DOI: 10.7717/peerj-cs.86 and https://www.force11.org/software-citation-principles • Contains: principles (general statements), use cases (where the principles should apply), discussion (suggestions on how to apply principles)
- 7. Principle 1. Importance • Software should be considered a legitimate and citable product of research. Software citations should be accorded the same importance in the scholarly record as citations of other research products, such as publications and data; they should be included in the metadata of the citing work, for example in the reference list of a journal article, and should not be omitted or separated. Software should be cited on the same basis as any other research product such as a paper or a book, that is, authors should cite the appropriate set of software products just as they cite the appropriate set of papers.
- 8. Principle 2. Credit and Attribution • Software citations should facilitate giving scholarly credit and normative, legal attribution to all contributors to the software, recognizing that a single style or mechanism of attribution may not be applicable to all software. Principle 3. Unique Identification • A software citation should include a method for identification that is machine actionable, globally unique, interoperable, and recognized by at least a community of the corresponding domain experts, and preferably by general public researchers.
- 9. Principle 4. Persistence • Unique identifiers and metadata describing the software and its disposition should persist – even beyond the lifespan of the software they describe. Principle 5. Accessibility • Software citations should facilitate access to the software itself and to its associated metadata, documentation, data, and other materials necessary for both humans and machines to make informed use of the referenced software. Principle 6. Specificity • Software citations should facilitate identification of, and access to, the specific version of software that was used. Software identification should be as specific as necessary, such as using version numbers, revision numbers, or variants such as platforms.
- 10. Example 1: Make your software citable • Publish it – if it’s on GitHub, follow steps in https://guides.github.com/activities/citable-code/ • Otherwise, submit it to zenodo or figshare, with appropriate metadata (including authors, title, …, citations of … & software that you use) • Get a DOI • Create a CITATION file, update your README, tell people how to cite • Note: citation principles also work for accessible commercial software, not just open source • Also, can write a software paper and ask people to cite that (but this is secondary, just since our current system doesn’t work well)
- 11. Example 2: Cite someone else’s software in a paper • Check for a CITATION file or README; if this says how to cite the software itself, do that • If not, do your best following the principles • Try to include all contributors to the software (maybe by just naming the project) • Try to include a method for identification that is machine actionable, globally unique, interoperable – perhaps a URL to a release, a company product number • If there’s a landing page that includes metadata, point to that, not directly to the software (e.g. the GitHub repo URL) • Include specific version/release information • If there’s a software paper, can cite this too, but not in place of citing the software
- 12. Examples of poor citations • Mandatory citations for commercial software, with no machine actionable unique identifier (Principle 3) and no persistent identifiers and metadata (Principle 4) • The output for this paper was generated using SAS/STAT software, Version 14.1 of the SAS System for Unix. Copyright © 2018 SAS Institute Inc. SAS and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute Inc., Cary, NC, USA. • MATLAB and Statistics Toolbox Release 2012b, The MathWorks, Inc., Natick, Massachusetts, United States. • Recommended citation for general software, also with no authors (Principle 2) and no version (Principle 6) • HSL. A collection of Fortran codes for large scale scientific computation. http://www.hsl.rl.ac.uk/
- 13. Examples of better citations • Examples of citations of specific packages as recommended by the software platform they are distributed with that mostly implement the principles, but without persistent identifiers and metadata (Principle 4) • Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K. (2018). cluster: Cluster Analysis Basics and Extensions. R package version 2.0.7-1. • Emma J. Moore, Christopher D. Wensley, groupoids - a GAP package, 1.54, 29/11/2017, https://gap- packages.github.io/groupoids/ • Note: these are in different styles (format), but contain the same data
- 14. Examples of good citations • Eigen Project. (2017). Eigen [software] version 3.3.4 Available from https://bitbucket.org/eigen/eigen/ [accessed 2018-04-27] • Vince Knight, & Ria Baldevia. (2018, January 31). drvinceknight/Nashpy: v0.0.13 (Version v0.0.13). Zenodo. http://doi.org/10.5281/zenodo.1163694
- 15. Future steps for math software • Promote developers creating good citations • Provide metadata using CodeMeta (https://codemeta.github.io) or Citation File Format (CFF, https://citation-file-format.github.io) • Enhance swMath to promulgate those citations • swMath could have a generic citation for a software package • Note: identifiers and citations for packages (not versions) are also needed, and while this could be done by software papers, DataCite has an initial service that takes a package (e.g. a GitHub repo) and metadata, and returns a DOI • And citations for specific versions
- 16. Journal of Open Source Software (JOSS) • In the meantime, there’s JOSS • A developer friendly journal for research software packages • “If you've already licensed your code and have good documentation then we expect that it should take less than an hour to prepare and submit your paper to JOSS” • Everything is open: • Submitted/published paper: http://joss.theoj.org • Code itself: where is up to the author(s) • Reviews & process: https://github.com/openjournals/joss-reviews • Code for the journal itself: https://github.com/openjournals/joss • Zenodo archives JOSS papers and issues DOIs • First paper submitted 4 May 2016 • 31 May 2017: 111 accepted papers, 56 under review and pre-review • 6 July 2018: 320 accepted papers, 75 under review and pre-review
- 17. Working group status & next steps • Software Citation Working Group (co-chairs Smith, Katz, Niemeyer) ended May 2017 • Software Citation Implementation group (co-chairs Katz, Fenner, Chue Hong) started May 2017 • Want to join? Sign up on FORCE11 group page • https://www.force11.org/group/software-citation-implementation- working-group • Now starting up task forces: • CodeMeta • Guidelines for communities (disciplines) • Publisher adoption • Repository best practices • Sign up via GitHub: https://github.com/force11/force11-sciwg